package dr.evolution.datatype;
/**
* @author Marc A. Suchard
*/
public class HiddenCodons extends Codons implements HiddenDataType {
public static final String DESCRIPTION = "hiddenCodon";
public static final HiddenCodons UNIVERSAL_HIDDEN_2 = new HiddenCodons(GeneticCode.UNIVERSAL,2);
public static final HiddenCodons UNIVERSAL_HIDDEN_3 = new HiddenCodons(GeneticCode.UNIVERSAL,3);
/**
* Private constructor - DEFAULT_INSTANCE provides the only instance
*/
private HiddenCodons(GeneticCode geneticCode, int hiddenClassCount) {
super(geneticCode);
this.hiddenClassCount = hiddenClassCount;
}
/**
* returns an array containing the non-ambiguous states that this state represents.
*/
public boolean[] getStateSet(int state) {
boolean[] stateSet = new boolean[stateCount*hiddenClassCount];
if (!isAmbiguousState(state)) {
for(int h=0; h<hiddenClassCount; h++)
stateSet[h*stateCount + state] = true;
} else {
for (int i = 0; i < stateCount; i++) {
stateSet[i] = true;
}
}
return stateSet;
}
public int getStateCount() {
return stateCount*hiddenClassCount;
}
private int hiddenClassCount;
public int getHiddenClassCount() {
return hiddenClassCount;
}
}